zcat S2_H3K27me3_ChIP-seq-GSM480157_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bowtie-indexes/dm6 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bowtie-indexes/dm6.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort -  S2_H3K27me3_ChIP-seq-GSM480157.25mers.unique
zcat S2_H3K36me3_ChIP-seq-GSM480158_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bowtie-indexes/dm6 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bowtie-indexes/dm6.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort -  S2_H3K36me3_ChIP-seq-GSM480158.25mers.unique
zcat S2_H3K4me3_ChIP-seq-GSM480156-1_1.fastq.gz S2_H3K4me3_ChIP-seq-GSM480156-2_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bowtie-indexes/dm6 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bowtie-indexes/dm6.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort -  S2_H3K4me3_ChIP-seq-GSM480156.25mers.unique
zcat S2_Pol_II_ChIP-seq-GSM480159_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bowtie-indexes/dm6 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bowtie-indexes/dm6.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort -  S2_Pol_II_ChIP-seq-GSM480159.25mers.unique